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Li-Zhulanov NS, Zakharenko AL, Chepanova AA, Patel J, Zafar A, Volcho KP, Salakhutdinov NF, Reynisson J, Leung IKH, Lavrik OI. A Novel Class of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Contains the Octahydro-2 H-chromen-4-ol Scaffold. Molecules 2018; 23:E2468. [PMID: 30261631 PMCID: PMC6222798 DOI: 10.3390/molecules23102468] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/25/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that mends topoisomerase 1-mediated DNA damage. Tdp1 is a current inhibition target for the development of improved anticancer treatments, as its inhibition may enhance the therapeutic effect of topoisomerase 1 poisons. Here, we report a study on the development of a novel class of Tdp1 inhibitors that is based on the octahydro-2H-chromene scaffold. Inhibition and binding assays revealed that these compounds are potent inhibitors of Tdp1, with IC50 and KD values in the low micromolar concentration range. Molecular modelling predicted plausible conformations of the active ligands, blocking access to the enzymatic machinery of Tdp1. Our results thus help establish a structural-activity relationship for octahydro-2H-chromene-based Tdp1 inhibitors, which will be useful for future Tdp1 inhibitor development work.
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Affiliation(s)
- Nikolai S Li-Zhulanov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| | - Arina A Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ayesha Zafar
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Konstantin P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Nariman F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Olga I Lavrik
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
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Bashir Surfraz M, Fowkes A, Plante JP. A Semi-automated Approach to Create Purposeful Mechanistic Datasets from Heterogeneous Data: Data Mining Towards the in silico Predictions for Oestrogen Receptor Modulation and Teratogenicity. Mol Inform 2017; 36. [PMID: 28436609 DOI: 10.1002/minf.201600154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/16/2017] [Indexed: 12/14/2022]
Abstract
The need to find an alternative to costly animal studies for developmental and reproductive toxicity testing has shifted the focus considerably to the assessment of in vitro developmental toxicology models and the exploitation of pharmacological data for relevant molecular initiating events. We hereby demonstrate how automation can be applied successfully to handle heterogeneous oestrogen receptor data from ChEMBL. Applying expert-derived thresholds to specific bioactivities allowed an activity call to be attributed to each data entry. Human intervention further improved this mechanistic dataset which was mined to develop structure-activity relationship alerts and an expert model covering 45 chemical classes for the prediction of oestrogen receptor modulation. The evaluation of the model using FDA EDKB and Tox21 data was quite encouraging. This model can also provide a teratogenicity prediction along with the additional information it provides relevant to the query compound, all of which will require careful assessment of potential risk by experts.
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Affiliation(s)
- M Bashir Surfraz
- Granary Wharf House, 2 Canal Wharf, Holbeck, Leeds, LS11 5PS, United Kingdom
| | - Adrian Fowkes
- Granary Wharf House, 2 Canal Wharf, Holbeck, Leeds, LS11 5PS, United Kingdom
| | - Jeffrey P Plante
- Granary Wharf House, 2 Canal Wharf, Holbeck, Leeds, LS11 5PS, United Kingdom
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